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Conserved domains on  [gi|2132600167|emb|CAG8814427|]
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19005_t:CDS:2, partial [Gigaspora rosea]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 1-200 5.29e-129

Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


:

Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 361.49  E-value: 5.29e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRVEGKTFTCEFKYDGERGQIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAW 80
Cdd:cd07900    16 KPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLKPSVKSFILDSEIVAY 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNVE 160
Cdd:cd07900    96 DRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQFATSKDSEDTE 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2132600167 161 EIQAFLDESVKGSCEGLMVKILDGpESSYEPSKRSRNWLK 200
Cdd:cd07900   176 EIQEFLEEAVKNNCEGLMVKTLDS-DATYEPSKRSHNWLK 214
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 1-200 5.29e-129

Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 361.49  E-value: 5.29e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRVEGKTFTCEFKYDGERGQIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAW 80
Cdd:cd07900    16 KPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLKPSVKSFILDSEIVAY 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNVE 160
Cdd:cd07900    96 DRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQFATSKDSEDTE 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2132600167 161 EIQAFLDESVKGSCEGLMVKILDGpESSYEPSKRSRNWLK 200
Cdd:cd07900   176 EIQEFLEEAVKNNCEGLMVKTLDS-DATYEPSKRSHNWLK 214
PLN03113 PLN03113
DNA ligase 1; Provisional
 2-200 7.18e-88

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 273.40  E-value: 7.18e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   2 PTKSITEALDRVEGKTFTCEFKYDGERGQIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAWD 81
Cdd:PLN03113  377 PTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVAISRLKKPSVKSFILDCELVAYD 456

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  82 PEKNCLLPFQILSTRKRKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNVEE 161
Cdd:PLN03113  457 REKKKILPFQILSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEEDPGFFQFATAITSNDLEE 536

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2132600167 162 IQAFLDESVKGSCEGLMVKILDGpESSYEPSKRSRNWLK 200
Cdd:PLN03113  537 IQKFLDAAVDASCEGLIIKTLNK-DATYEPSKRSNNWLK 574
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 1-200 4.27e-80

ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.


Pssm-ID: 426028 [Multi-domain]  Cd Length: 203  Bit Score: 237.18  E-value: 4.27e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRvEGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAW 80
Cdd:pfam01068   5 KSFKSIEEALKK-FGGAFIAEYKYDGERAQIHK-DGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGEIVAV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRKDVKESDI--KVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASN 158
Cdd:pfam01068  83 DPETGEILPFQVLADRKKKKVDVEELaeKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVTKD 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2132600167 159 VEEIQAFLDESVKGSCEGLMVKildGPESSYEPSKRSRNWLK 200
Cdd:pfam01068 163 VEEAQEFLEEAISEGLEGLVVK---DPDSTYEPGKRGKNWLK 201
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 1-200 8.83e-71

DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273147 [Multi-domain]  Cd Length: 514  Bit Score: 223.35  E-value: 8.83e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRVeGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAW 80
Cdd:TIGR00574 173 ERAKSIEEALKKK-GNGFYVEYKYDGERVQVHK-DGDKFKIFSRRLENYTYQYPEIFTEFIKEAFPGIKSCILDGEMVAI 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRK-DVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNV 159
Cdd:TIGR00574 251 DPETGKPLPFGTLLRRKRKyDIKAMDQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILKPIPNRIEIAEMKIVSNV 330

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2132600167 160 EEIQAFLDESVKGSCEGLMVKILdgpESSYEPSKRSRNWLK 200
Cdd:TIGR00574 331 EELEKFLNEAISEGCEGLMLKDL---KSIYEPGKRGWLWLK 368
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
8-200 1.14e-50

ATP-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 168.95  E-value: 1.14e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   8 EALDRV-EGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIvkpGTKNFVLDCEIVAWDPEKnc 86
Cdd:COG1793   120 TLVDSPpDGGDWAYEPKWDGYRVQAHR-DGGEVRLYSRNGEDITDRFPELVEALRAL---PADDAVLDGEIVALDEDG-- 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  87 LLPFQILSTRK--RKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMnaSNVEEIQA 164
Cdd:COG1793   194 RPPFQALQQRLgrKRDVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHV--IDWGEGEA 271

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2132600167 165 FLDESVKGSCEGLMVKILDGPessYEPSKRSRNWLK 200
Cdd:COG1793   272 LFAAAREAGLEGVMAKRLDSP---YRPGRRSGDWLK 304
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 1-200 5.29e-129

Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 361.49  E-value: 5.29e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRVEGKTFTCEFKYDGERGQIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAW 80
Cdd:cd07900    16 KPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLKPSVKSFILDSEIVAY 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNVE 160
Cdd:cd07900    96 DRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQFATSKDSEDTE 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2132600167 161 EIQAFLDESVKGSCEGLMVKILDGpESSYEPSKRSRNWLK 200
Cdd:cd07900   176 EIQEFLEEAVKNNCEGLMVKTLDS-DATYEPSKRSHNWLK 214
PLN03113 PLN03113
DNA ligase 1; Provisional
 2-200 7.18e-88

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 273.40  E-value: 7.18e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   2 PTKSITEALDRVEGKTFTCEFKYDGERGQIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAWD 81
Cdd:PLN03113  377 PTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVAISRLKKPSVKSFILDCELVAYD 456

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  82 PEKNCLLPFQILSTRKRKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNVEE 161
Cdd:PLN03113  457 REKKKILPFQILSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEEDPGFFQFATAITSNDLEE 536

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2132600167 162 IQAFLDESVKGSCEGLMVKILDGpESSYEPSKRSRNWLK 200
Cdd:PLN03113  537 IQKFLDAAVDASCEGLIIKTLNK-DATYEPSKRSNNWLK 574
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 1-200 4.27e-80

ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.


Pssm-ID: 426028 [Multi-domain]  Cd Length: 203  Bit Score: 237.18  E-value: 4.27e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRvEGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAW 80
Cdd:pfam01068   5 KSFKSIEEALKK-FGGAFIAEYKYDGERAQIHK-DGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGEIVAV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRKDVKESDI--KVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASN 158
Cdd:pfam01068  83 DPETGEILPFQVLADRKKKKVDVEELaeKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVTKD 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2132600167 159 VEEIQAFLDESVKGSCEGLMVKildGPESSYEPSKRSRNWLK 200
Cdd:pfam01068 163 VEEAQEFLEEAISEGLEGLVVK---DPDSTYEPGKRGKNWLK 201
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 1-200 8.83e-71

DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273147 [Multi-domain]  Cd Length: 514  Bit Score: 223.35  E-value: 8.83e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRVeGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNFVLDCEIVAW 80
Cdd:TIGR00574 173 ERAKSIEEALKKK-GNGFYVEYKYDGERVQVHK-DGDKFKIFSRRLENYTYQYPEIFTEFIKEAFPGIKSCILDGEMVAI 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRK-DVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNV 159
Cdd:TIGR00574 251 DPETGKPLPFGTLLRRKRKyDIKAMDQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILKPIPNRIEIAEMKIVSNV 330

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2132600167 160 EEIQAFLDESVKGSCEGLMVKILdgpESSYEPSKRSRNWLK 200
Cdd:TIGR00574 331 EELEKFLNEAISEGCEGLMLKDL---KSIYEPGKRGWLWLK 368
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 5-200 4.99e-57

Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185711 [Multi-domain]  Cd Length: 207  Bit Score: 178.89  E-value: 4.99e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   5 SITEALDRvEGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPgtKNFVLDCEIVAWDPEk 84
Cdd:cd07901    15 SVEEALIK-EGGEAAVEYKYDGIRVQIHK-DGDEVRIFSRRLEDITNALPEVVEAVRELVKA--EDAILDGEAVAYDPD- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  85 NCLLPFQILSTR-KRK-DVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEgKFSFARHMNASNVEEI 162
Cdd:cd07901    90 GRPLPFQETLRRfRRKyDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPETE-AILLAPRIVTDDPEEA 168

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2132600167 163 QAFLDESVKGSCEGLMVKILDGPessYEPSKRSRNWLK 200
Cdd:cd07901   169 EEFFEEALEAGHEGVMVKSLDSP---YQAGRRGKNWLK 203
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 1-200 1.18e-56

Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185709 [Multi-domain]  Cd Length: 201  Bit Score: 177.53  E-value: 1.18e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRvEGKTFTCEFKYDGERGQIHLLEdGTAKIYSRNLEDSSMKFPDVLEILSSIVKPgtknFVLDCEIVAW 80
Cdd:cd07898     7 HPEESAEAAKAK-KPAAAWVEDKYDGIRAQVHKDG-GRVEIFSRSLEDITDQFPELAAAAKALPHE----FILDGEILAW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNC--LLPFQILSTRKRKDVKESDIKVsvCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASN 158
Cdd:cd07898    81 DDNRGLpfSELFKRLGRKFRDKFLDEDVPV--VLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAPALPVES 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2132600167 159 VEEIQAFLDESVKGSCEGLMVKildGPESSYEPSKRSRNWLK 200
Cdd:cd07898   159 AEELEAAFARARARGNEGLMLK---DPDSPYEPGRRGLAWLK 197
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 5-200 8.14e-54

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 180.55  E-value: 8.14e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   5 SITEALDRVEGKTFtCEFKYDGERGQIHLLeDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPgtKNFVLDCEIVAWDPEK 84
Cdd:PRK01109  238 SPKEILKKMGGEAL-VEYKYDGERAQIHKK-GDKVKIFSRRLENITHQYPDVVEYAKEAIKA--EEAIVEGEIVAVDPET 313

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  85 NCLLPFQILSTRKRK-DVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEgKFSFARHMNASNVEEIQ 163
Cdd:PRK01109  314 GEMRPFQELMHRKRKyDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND-KVKLAERIITDDVEELE 392

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2132600167 164 AFLDESVKGSCEGLMVKILdGPESSYEPSKRSRNWLK 200
Cdd:PRK01109  393 KFFHRAIEEGCEGLMAKSL-GKDSIYQAGARGWLWIK 428
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
8-200 1.14e-50

ATP-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 168.95  E-value: 1.14e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   8 EALDRV-EGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIvkpGTKNFVLDCEIVAWDPEKnc 86
Cdd:COG1793   120 TLVDSPpDGGDWAYEPKWDGYRVQAHR-DGGEVRLYSRNGEDITDRFPELVEALRAL---PADDAVLDGEIVALDEDG-- 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  87 LLPFQILSTRK--RKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMnaSNVEEIQA 164
Cdd:COG1793   194 RPPFQALQQRLgrKRDVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHV--IDWGEGEA 271

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2132600167 165 FLDESVKGSCEGLMVKILDGPessYEPSKRSRNWLK 200
Cdd:COG1793   272 LFAAAREAGLEGVMAKRLDSP---YRPGRRSGDWLK 304
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 7-200 5.19e-42

Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185713 [Multi-domain]  Cd Length: 225  Bit Score: 141.18  E-value: 5.19e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   7 TEALDRVEGKTFTCEFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLE------ILSSIVKPGTKNFVLDCEIVAW 80
Cdd:cd07903    24 YVEIKLLKGKPFYIETKLDGERIQLHK-DGNEFKYFSRNGNDYTYLYGASLTpgsltpYIHLAFNPKVKSCILDGEMVVW 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKrKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNVE 160
Cdd:cd07903   103 DKETKRFLPFGTLKDVA-KLREVEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPIPGRLEVVKRTEASTKE 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2132600167 161 EIQAFLDESVKGSCEGLMVKILDgpeSSYEPSKRSRNWLK 200
Cdd:cd07903   182 EIEEALNEAIDNREEGIVVKDLD---SKYKPGKRGGGWIK 218
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 21-200 5.32e-34

Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining.


Pssm-ID: 185715 [Multi-domain]  Cd Length: 190  Bit Score: 119.18  E-value: 5.32e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  21 EFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKpgtKNFVLDCEIVAWDPEKnclLP-FQILSTRKRK 99
Cdd:cd07906    21 EIKWDGYRALARV-DGGRVRLYSRNGLDWTARFPELAEALAALPV---RDAVLDGEIVVLDEGG---RPdFQALQNRLRL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167 100 DVKESDiKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHmnasNVEEIQAFLDESVKGSCEGLMV 179
Cdd:cd07906    94 RRRLAR-TVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEH----FEGGGAALFAAACELGLEGIVA 168

                         170       180
                  ....*....|....*....|.
gi 2132600167 180 KILDgpeSSYEPSKRSRNWLK 200
Cdd:cd07906   169 KRAD---SPYRSGRRSRDWLK 186
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 2-200 1.62e-31

Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many active site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185712 [Multi-domain]  Cd Length: 213  Bit Score: 113.59  E-value: 1.62e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   2 PTKSITEALDRVEgKTFTCEFKYDGERGQIHLLEDgTAKIYSRNLED-SSMKFPDVLEILSSIVkPGTKNFVLDCEIVAW 80
Cdd:cd07902    21 ACKSVEDAMKKCP-NGMYAEIKYDGERVQVHKQGD-NFKFFSRSLKPvLPHKVAHFKDYIPKAF-PHGHSMILDSEVLLV 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKNCLLPFQILSTRKRKDVKESdikvSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNVE 160
Cdd:cd07902    98 DTKTGKPLPFGTLGIHKKSAFKDA----NVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNRIMLSEMKFVKKAD 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2132600167 161 EIQAFLDESVKGSCEGLMVKILDGPessYEPSKrsRNWLK 200
Cdd:cd07902   174 DLSAMIARVIKEGLEGLVLKDLKSV---YEPGK--RHWLK 208
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 1-200 2.75e-27

Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.


Pssm-ID: 185708 [Multi-domain]  Cd Length: 207  Bit Score: 102.63  E-value: 2.75e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRVEgkTFTCEFKYDGERGQIhLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIvkpgTKNFVLDCEIVAW 80
Cdd:cd07897    11 HPLEDDPEDLGDPS--DWQAEWKWDGIRGQL-IRRGGEVFLWSRGEELITGSFPELLAAAEAL----PDGTVLDGELLVW 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  81 DPEKncLLPFQILSTR-KRKDV-KESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVE-GKFSFARHMNAS 157
Cdd:cd07897    84 RDGR--PLPFNDLQQRlGRKTVgKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPpPRLDLSPLIAFA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2132600167 158 NVEEIQAFLDESVKGSCEGLMVKILDGPessYEPSKRSRNWLK 200
Cdd:cd07897   162 DWEELAALRAQSRERGAEGLMLKRRDSP---YLVGRKKGDWWK 201
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 1-200 2.37e-22

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 93.49  E-value: 2.37e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   1 HPTKSITEALDRVEGKTfTCEFKYDGERGQIHllEDG-TAKIYSRNLEDSSMKFPDVLEILSSIvkPGTKnFVLDCEIVA 79
Cdd:PRK03180  190 QTATSVAEALARLGGPA-AVEAKLDGARVQVH--RDGdDVRVYTRTLDDITARLPEVVEAVRAL--PVRS-LVLDGEAIA 263

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  80 WDPEkNCLLPFQILSTR--KRKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREhlynAFQEVEGKFSFARHMNAS 157
Cdd:PRK03180  264 LRPD-GRPRPFQVTASRfgRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLA----ALDALVPAAHRVPRLVTA 338

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2132600167 158 NVEEIQAFLDESVKGSCEGLMVKILDGPessYEPSKRSRNWLK 200
Cdd:PRK03180  339 DPAAAAAFLAAALAAGHEGVMVKSLDAP---YAAGRRGAGWLK 378
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 21-200 2.06e-20

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 87.97  E-value: 2.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  21 EFKYDGERGQIhLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIvkPGtkNFVLDCEIVAWDPEKNCLLPFQILSTR-KRK 99
Cdd:PRK09247  230 EWKWDGIRVQL-VRRGGEVRLWSRGEELITERFPELAEAAEAL--PD--GTVLDGELLVWRPEDGRPQPFADLQQRiGRK 304

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167 100 DVKESDIK-VSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVE-GKFSFARHMNASNVEEIQAFLDESVKGSCEGL 177
Cdd:PRK09247  305 TVGKKLLAdYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPdPRLDLSPLVPFSDWDELAALRAAARERGVEGL 384

                         170       180
                  ....*....|....*....|...
gi 2132600167 178 MVKILDGPessYEPSKRSRNWLK 200
Cdd:PRK09247  385 MLKRRDSP---YLVGRKKGPWWK 404
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 21-200 1.90e-19

DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.


Pssm-ID: 274295 [Multi-domain]  Cd Length: 298  Bit Score: 83.89  E-value: 1.90e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  21 EFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPDV------LEILSSIvkpgtknfvLDCEIVAWDpeKNCLLPFQILS 94
Cdd:TIGR02779  17 EVKYDGYRCLARI-EGGKVRLISRNGHDWTEKFPILaaalaaLPILPAV---------LDGEIVVLD--ESGRSDFSALQ 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  95 TRKRKDvKESDIkvsvCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHMNASNvEEIQAFLDESVKGSC 174
Cdd:TIGR02779  85 NRLRAG-RDRPA----TYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRYSVHFE-GDGQALLEAACRLGL 158

                         170       180
                  ....*....|....*....|....*.
gi 2132600167 175 EGLMVKILDGPessYEpSKRSRNWLK 200
Cdd:TIGR02779 159 EGVVAKRRDSP---YR-SGRSADWLK 180
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 6-200 3.76e-19

Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity.


Pssm-ID: 185704 [Multi-domain]  Cd Length: 182  Bit Score: 80.54  E-value: 3.76e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   6 ITEALDRVEGKTFTCEFKYDGERGQIHLLEDGTaKIYSRNLEDSSMKFPDVLEILSSIVKPGtknFVLDCEIVAWDPEKN 85
Cdd:cd06846     9 EEALSEYDEQDEYYVQEKYDGKRALIVALNGGV-FAISRTGLEVPLPSILIPGRELLTLKPG---FILDGELVVENREVA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  86 cllpfqilstrkrkdvkesdiKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVE----GKFSFARHMNASNvEE 161
Cdd:cd06846    85 ---------------------NPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEgldpVKLVPLENAPSYD-ET 142

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2132600167 162 IQAFLDESVKGSCEGLMVKILDGPESsyEPSKRSRNWLK 200
Cdd:cd06846   143 LDDLLEKLKKKGKEGLVFKHPDAPYK--GRPGSSGNQLK 179
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 10-200 1.01e-17

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 80.43  E-value: 1.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  10 LDRVEGKTFTCEFKYDGERgQIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIvkpGTKNFVLDCEIVAWDPEKnclLP 89
Cdd:PRK09632  471 VAGLKASQWAFEGKWDGYR-LLAEADHGALRLRSRSGRDVTAEYPELAALAEDL---ADHHVVLDGEIVALDDSG---VP 543

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  90 -FQILSTRKRKdvkesdikVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGkfsfaRHMNASNVEEIQAFLDE 168
Cdd:PRK09632  544 sFGLLQNRGRD--------TRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSGGS-----LTVPPLLPGDGAEALAY 610

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2132600167 169 SVKGSCEGLMVKILDgpeSSYEPSKRSRNWLK 200
Cdd:PRK09632  611 SRELGWEGVVAKRRD---STYQPGRRSSSWIK 639
Adenylation_DNA_ligase_Fungal cd08039
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ...
 4-200 3.99e-17

Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. This model characterizes the adenylation domain of this group of uncharacterized fungal proteins. It is not known whether these proteins also contain an OB-fold domain.


Pssm-ID: 185716 [Multi-domain]  Cd Length: 235  Bit Score: 76.29  E-value: 3.99e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167   4 KSITEALDRVEGKTFTCEFKYDGERGQIHL-LEDGTA--KIYSRNLEDSSMKFPDVLEILS---SIVKPGTK---NFVLD 74
Cdd:cd08039    10 RSIKHCCKMIGSRRMWVETKYDGEYCQIHIdLSKDSSpiRIFSKSGKDSTADRAGVHSIIRkalRIGKPGCKfskNCILE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  75 CEIVAWDPEKNCLLPFQilstRKRKDVK----------ESDIKVSVCLYA--FDLLYLNGESLLQKSFTERREHLYNAFQ 142
Cdd:cd08039    90 GEMVVWSDRQGKIDPFH----KIRKHVErsgsfigtdnDSPPHEYEHLMIvfFDVLLLDDESLLSKPYSERRDLLESLVH 165

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2132600167 143 EVEGK--------FSFARHMNASNVEEIQAfldESVKGSCEGLMVKILDGPESSYEPSKRSRN--WLK 200
Cdd:cd08039   166 VIPGYaglserfpIDFSRSSGYERLRQIFA---RAIAERWEGLVLKGDEEPYFDLFLEQGSFSgcWIK 230
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 21-200 2.64e-16

Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185714 [Multi-domain]  Cd Length: 194  Bit Score: 73.43  E-value: 2.64e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  21 EFKYDGERGqIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGtknFVLDCEIVAWDPEKnclLPFQILSTR---K 97
Cdd:cd07905    21 EPKWDGFRC-LAFRDGDEVRLQSRSGKPLTRYFPELVAAARALLPPG---CVLDGELVVWRGGR---LDFDALQQRihpA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  98 RKDVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGKFSFARHmnASNVEEIQAFLDESVKGSCEGL 177
Cdd:cd07905    94 ASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPA--TTDRAEAREWLEEFEGAGLEGV 171

                         170       180
                  ....*....|....*....|...
gi 2132600167 178 MVKILDGPessYEPSKRSrnWLK 200
Cdd:cd07905   172 VAKRLDGP---YRPGERA--MLK 189
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 21-200 1.53e-14

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 71.09  E-value: 1.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  21 EFKYDGERGQIHLlEDGTAKIYSRNLEDSSMKFPdvlEILSSIVKPGTKNFVLDCEIVAWDPEKnclLP-FQIL----ST 95
Cdd:PRK05972  254 EIKFDGYRILARI-EGGEVRLFTRNGLDWTAKLP---ALAKAAAALGLPDAWLDGEIVVLDEDG---VPdFQALqnafDE 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  96 RKRKDVkesdikvsVClYAFDLLYLNGESLLQKSFTERREHLYNAFQEVEGK-FSFARHMNASNveeiQAFLDESVKGSC 174
Cdd:PRK05972  327 GRTEDL--------VY-FAFDLPFLGGEDLRELPLEERRARLRALLEAARSDrIRFSEHFDAGG----DAVLASACRLGL 393

                         170       180
                  ....*....|....*....|....*.
gi 2132600167 175 EGLMVKILDGPessYEpSKRSRNWLK 200
Cdd:PRK05972  394 EGVIGKRADSP---YV-SGRSEDWIK 415
ligD PRK09633
DNA ligase D;
21-200 1.62e-12

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 65.45  E-value: 1.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  21 EFKYDGERGqIHLLEDGTAKIYSRNLEDSSMKFPDVLEILSSIVKPGTKNF--VLDCEIVAW-DPEKNCLLPFQILSTRK 97
Cdd:PRK09633   21 EVKYDGFRC-LLIIDETGITLISRNGRELTNTFPEIIEFCESNFEHLKEELplTLDGELVCLvNPYRSDFEHVQQRGRLK 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  98 RKDV-KESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEVegKFSFARHMNASNV-------EEIQAFLDES 169
Cdd:PRK09633  100 NTEViAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAA--KLPASPDPYAKARiqyipstTDFDALWEAV 177

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2132600167 170 VKGSCEGLMVKILDgpeSSYEPSKRSRNWLK 200
Cdd:PRK09633  178 KRYDGEGIVAKKKT---SKWLENKRSKDWLK 205
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 18-200 3.59e-12

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 63.24  E-value: 3.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  18 FTCEFKYDGERgQIHLLEDGTAKIYSRNLEDSSMKFPdvlEILSSIVKPGTknfVLDCEIVAWDPEKNCllPFQILSTRK 97
Cdd:PRK07636   20 YITEPKFDGIR-LIASKNNGLIRLYTRHNNEVTAKFP---ELLNLDIPDGT---VLDGELIVLGSTGAP--DFEAVMERF 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  98 RkdVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLYNAFQEvegkfsfarHMNASNVEEIQ----AFLDESVKGS 173
Cdd:PRK07636   91 Q--SKKSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLP---------HPNVKIIEGIEghgtAYFELVEERE 159

                         170       180
                  ....*....|....*....|....*..
gi 2132600167 174 CEGLMVKildGPESSYEPSKRSRNWLK 200
Cdd:PRK07636  160 LEGIVIK---KANSPYEINKRSDNWLK 183
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 43-200 7.53e-11

DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; it only represents the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274293 [Multi-domain]  Cd Length: 552  Bit Score: 60.41  E-value: 7.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  43 SRNLEDSSMKFPDVLEILSSIvkpGTKNFVLDCEIVAWDpeKNCLLPFQILstrkrKDVKESDIKVSVCLYAFDLLYLNG 122
Cdd:TIGR02776   1 TRNGHDWTKRFPEIVKALALL---KLLPAWIDGEIVVLD--ERGRADFAAL-----QNALSAGASRPLTYYAFDLLFLSG 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2132600167 123 ESLLQKSFTERREHLYNAFQEVEGKfsfARHMNASNVEEIQAFLDESVKGSCEGLMVKILDGPESsyepSKRSRNWLK 200
Cdd:TIGR02776  71 EDLRDLPLEERKKRLKQLLKAQDEP---AIRYSDHFESDGDALLESACRLGLEGVVSKRLDSPYR----SGRSKDWLK 141
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
 23-200 2.66e-08

Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active-site residues.


Pssm-ID: 185707 [Multi-domain]  Cd Length: 174  Bit Score: 51.41  E-value: 2.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  23 KYDGERGQIhlleDGTaKIYSRNLEdsSMKFPDVLeilssivkpgTKNF---VLDCEIVAwdpEKNCllpFQILSTRKRK 99
Cdd:cd07896    23 KLDGVRAYW----DGK-QLLSRSGK--PIAAPAWF----------TAGLppfPLDGELWI---GRGQ---FEQTSSIVRS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167 100 DVKESDIKVSVCLYAFDLLYLNGesllqkSFTERREHLYNAFQEVEGKF-SFARHMNASNVEEIQAFLDESVKGSCEGLM 178
Cdd:cd07896    80 KKPDDEDWRKVKFMVFDLPSAKG------PFEERLERLKNLLEKIPNPHiKIVPQIPVKSNEALDQYLDEVVAAGGEGLM 153

                         170       180
                  ....*....|....*....|..
gi 2132600167 179 vkiLDGPESSYEPsKRSRNWLK 200
Cdd:cd07896   154 ---LRRPDAPYET-GRSDNLLK 171
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 21-195 1.01e-07

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 51.05  E-value: 1.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  21 EFKYDGERgqIHLLEDGTA-KIYSRNLEDSSMKFPDVLEILSSIVKPgtkNFVLDCEIVAWDPEKnclLPFQILSTR--- 96
Cdd:PRK08224   29 EPKWDGFR--CLVFRDGDEvELGSRNGKPLTRYFPELVAALRAELPE---RCVLDGEIVVARDGG---LDFEALQQRihp 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  97 --KRkdVKESDIKVSVCLYAFDLLYLNGESLLQKSFTERREHLyNAFQEVEGKFSFARHmnASNVEEIQAFLDESVKGSC 174
Cdd:PRK08224  101 aaSR--VRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAAL-EAAAAGSGPVHLTPA--TTDPATARRWFEEFEGAGL 175

                         170       180
                  ....*....|....*....|.
gi 2132600167 175 EGLMVKILDGPessYEPSKRS 195
Cdd:PRK08224  176 DGVIAKPLDGP---YQPGKRA 193
PRK09125 PRK09125
DNA ligase; Provisional
 91-200 6.56e-04

DNA ligase; Provisional


Pssm-ID: 181662 [Multi-domain]  Cd Length: 282  Bit Score: 39.46  E-value: 6.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2132600167  91 QILSTRKRKDVKESDIKvSVCLYAFDLLYLNGesllqkSFTERrehLYNAFQEVEGK----FSFARHMNASNVEEIQAFL 166
Cdd:PRK09125   99 AISSIVRDKTPDDAAWR-KVRFMVFDLPDAPG------DFEER---LAVLKKLLAKLpspyIKIIEQIRVRSEAALQQFL 168

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2132600167 167 DESVKGSCEGLMVKildGPESSYEPsKRSRNWLK 200
Cdd:PRK09125  169 DQIVAAGGEGLMLH---RPDAPYEA-GRSDDLLK 198
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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